CoreBook et la Cyber-carothèque nationale : deux outils pour bancariser des métadonnées riches lors des opérations de carottage scientifique (continental, marin, glaciaires)

International audienc

The French NATIONAL CYBER CORE REPOSITORY: a user-oriented approach to promote the referencing of scientific cores

PosterInternational audienceIn plaeosciences the question of data management is made sensitive by the need of preserving and managing high value fragile geological samples: cores. Large international scientific programs, such as IODP or ICDP led intense effort for such, proposing detailed high standard work- and dataflows. However many paleoscience results derived from small-scale research programs in which data and sample management are too often managed only locally – when they are. In France a national effort is currently led to develop an integrated system to curate ice and sediment cores. Under the umbrella of the national excellence equipment program CLIMCOR, we launched a reflexion about core curating and the management of associated fieldwork data. Our aim was then to preserve all data from fieldwork in an integrated cyber-environment. To do so, our demarche was conducted through an intimate relationship with field operators and laboratory core curators in order to propose user-oriented solutions. We built a single web portal that is used as a national hub from any team’s data and to international standards (IGSNs, INSPIRE) and databases (IMLGS). For legacy samples, this requires the establishment of a dedicated cores list with associated metadata. However, for forthcoming core data, we developed a mobile application to capture technical and scientific data directly on the field. This application is linked with a unique coring-tools library and is adapted to most coring devices (gravity, drilling, percussion etc.) including multiple sections and holes coring operations. In this paper, we present the architecture of the integrated system, future perspectives and the approach we adopted to reach our goals. We will also present our mobile application through didactic examples

Le couple CoreBook / Cyber-Carothèque Nationale : un système de collecte et de gestion d’information dédié aux carottes sédimentaires marines et continentales.

PosterInternational audienceLa gestion des données constitue l’un des défis de l’Open science dans le contexte de la loi « Pour une république numérique ». Ceci est particulièrement important dans le domaine des sciences de la Terre et de l’environnement dans lequel la multiplication des échantillons de terrain et de mesures qui sont réalisées sur chaque conduit à une croissance exponentielle du nombre de données. Dans le cas de l’étude des carottes sédimentaires, l’engouement pour les méthodes paléoenvironnementales, pour répondre à des problématiques variées allant des chroniques de contaminations récentes aux évolutions climatiques pluriséculaires à plurimillénaire, voire plus, participe de cette croissance. Or, l’absence de systèmes d’information dédiée ne permet pas de capitaliser sur cette grande richesse en reliant les données entre elles.Dans cette contribution, nous présentons un système développé dans le cadre du programme Equipex CLIMCOR afin de bancariser les informations de terrain collectées lors du prélèvement de carottes sédimentaire. Ce système est constitué de deux modules : i) CoreBook, qui est une application mobile de collecte d’information sous Android et ii) la Cyber-carothèque nationale (Base MySQL), qui est un portail d’import, de consultation et de diffusion des informations.CoreBook a été pensé pour être embarquée sur une tablette durcie du commerce. Elle apporte une plus-value lors des opérations de carottage sur le terrain. Il comprend notamment des fonctionnalités comme le repérage des carottages précédents, une aide à la navigation et aux opérations d’ancrage ou encore la visualisation en coupe des carottages multi-sections et/ou multi-trous, ou en carte des carottages simple section. Optimisé pour la carottage multi-sections multi-séquences, il est adapté à tout type de méthode de carottage (carottier russe, gravitaire, piston stationnaire, etc.). Chaque entité de recherche (labo) a la possibilité de créer des configurations de matériels dans le portail « Cyber-carothèque » en constituant un référentiel qu’il retrouvera dans le CoreBook ; ce référentiel facilite la sélection d’outils une fois sur le terrain et associe automatiquement les paramètres de carottage et d’outils aux futurs échantillons ce qui permet de gagner en précision et qualité. Les données collectées par CoreBook sont directement synchronisables avec la cyber-carothèque. Un format d’échange permettra également d’alimenter les bases de données locales de laboratoire. La cyber-carothèque permet de gérer les configurations matérielles des entités de recherche. Elle recueille les métadonnées des opérations de prélèvement de carottes, soit via CoreBook, soit via un fichier d’import respectant un format spécifique. Interopérable, elle est capable, via des web-services, de moissonner des bases existantes et d’être moissonnée par celles-ci par des protocoles standardisés (OGC WFS).Une fois entrée dans la Cyber-carothèque, chaque échantillon reçoit un identifiant unique au format international IGSN. Equivalent d’un DOI pour les échantillons géologiques, cet identifiant permet de tracer la carotte et les opérations de terrain ayant permis de la prélever, à chaque fois qu’elle est utilisée pour une publication ou intégrée dans un système d’information. Il s’agit d’une étape préalable indispensable vers la bancarisation, la qualité, le partage et la réutilisabilité des données.Pour l’utilisateur final, la Cyber-carothèque offre des fonctionnalités de recherche et constitue une base de référence, structurée, ouverte et standardisé permettant de connaître les échantillons déjà prélevés dans une région donnée, ou encore de suivre l’activité d’un groupe de chercheur ou d’une entité de recherche. En prenant le problème de la gestion des données à la base, au niveau des opérations de terrain, le système CoreBook & Cyber-carothèque fournit à la communauté scientifique nationale un socle solide pour développer des bases de données, soit pour la gestion interne des données et/ou des échantillons, soit pour évoluer vers des systèmes plus intégrés en associant de données analytiques. La Cyber-carothèque est accessible à l’adresse : https://cybercarotheque.fr/index.php, on y trouve notamment le lien et les instructions pour télécharger l’application CoreBook

How to turn kilos of mud into megabytes of data? 10 years of efforts in curating lake sediment cores and their associated results

International audienceHere we present a series of connected efforts aiming at curating sediment cores and their related data. Far to be isolated, these efforts were conducted within national structured projects and led to the development of digital solutions and good practices in-line with international standards and practices.Our efforts aimed at ensuring FAIR-compatible practices (Plomp, 2020; Wilkinson et al., 2016) throughout the life cycle of sediment cores, from fieldwork to published data. We adopted a step-by-step, bottom-up strategy to formalize a dataflow, mirroring our workflow. We hence created a fieldwork mobile application (CoreBook) to gather information during coring operations and inject them toward the French national virtual core repository “Cyber-Carothèque Nationale” (CCN). At this stage, the allocation of an international persistent unique identifier was crucial and we naturally chose the IGSN.Beyond the traceability of samples, the curation of analysis data remains challenging. Most international repository (e.g. NOAA palaeo-data, PANGAEA) have taken the problem from the top by offering facilities to display published dataset with persistant unique identifier (DOI). Yet, those data are only a fraction of the gross amount of acquired data. Moreover, those repositories have very low requirements when it comes to the preservation and display of metadata, in particular analytical parameters, but also fieldwork data which are essential for data reusability. Finally, these repositories do not permit to get a synoptic view on the several strata of analyses that have been conducted on the same core through different research programs and publications. A partial solution is proposed by the eLTER metadata standard DEIMS, which offers a discovery interface of rich metadata. In order to bridge the gap between generalist data repositories and samples display systems (such as CCN, but also IMLGS, to cite an international system), we developed a data repository and visualizer dedicated to the re-use of lake sediment cores, samples and sampling locations (ROZA Retro-Observatory of the Zone Atelier). This system is still a prototype but opens yet interesting perspectives.Finally, the digital evolution of science allows the worldwide diffusion of data processing freewares. In that framework, we developed “Serac” an open-source R package to establish radionuclide-based age models following the most common sedimentation hypotheses (serac,). By implementing within this R package the input of a rich metadata file that gathers links to IGSN and other quality metadata, we are linking fieldwork metadata, the physical storage of the core and the analytical metadata. Indeed, Serac also stores data processing procedure in a standardized way.. We hence think that the development of such softwares could help in the spreading of good practices in data curation and favour the use of unique identifiers.By tackling all aspects of data creation and curation throughout a lake sediment core life cycle, we are now able to propose a theoretical model of data curation for this particular type of sample that could serve as the sole for further developments of integrated data curation systems.https://doi.org/10.5194/egusphere-egu21-1503

From core referencing to data re-use: two French national initiatives to reinforce paleodata stewardship (National Cyber Core Repository and LTER France Retro-Observatory)

PosterInternational audienceManaging paleoscience data is highly challenging to the multiplicity of actors in play, types of sampling, analysis, post-analysis treatments, statistics etc. However, a well-structured curating of data would permit innovative developments based on data and/or sample re-use, such as meta-analysis or the development of new proxies on previously studied cores. In this paper, we will present two recent initiatives that allowed us tackling this objective at a French national level: the “National Cyber Core Repository” (NCCR) and the “LTER-France retro-observatory” (ROZA).NCCR was developed under the umbrella of the French National Center fo Coring and Drilling (C2FN) thanks to the national excellence equipment project CLIMCOR. It aims at gathering on a unique website the locations and metadata of any scientific coring/drilling performed by French teams or using French facilities, whatever the type of archive it is (lake/marine sediment; ice etc.). It uses international standard, notably IGSN (for samples), ORCID (for persons) and DOI (for campaigns). NCC follows the INSPIRE ISO 19115 standard in order to catalogue the data. For continental sediment, NCCR may be fed directly on the field through a specifically developed mobile application.Based on NCCR, further initiatives may be led. In particular, under the umbrella of LTER-France (Long Term Ecological Research), we developed ROZA in order to facilitate the re-use of data and samples. Here the idea is to capitalise the knowledge on a given lake from which several sediment cores can be taken through time. In that aim we selected at least one lake from each of the 13 areas composing the network LTER-France. To enter the database, a set of mandatory data must be provided under a pre-determined format. In that case, the insertion of ROZA within the network LTER will favor to use of paleodata by non-paleodata scientists, in particular ecologists

From the field to the database: a user-oriented approach to promote cyber-curating of scientific continental drilling cores

International audienceManaging scientific data is probably one the most challenging issues in modern science. In plaeosciences the question is made even more sensitive with the need of preserving and managing high value fragile geological samples: cores. Large international scientific programs, such as IODP or ICDP led intense effort to solve this problem and proposed detailed high standard work- and dataflows thorough core handling and curating. However many paleoscience results derived from small-scale research programs in which data and sample management is too often managed only locally – when it is… In this paper we present a national effort leads in France to develop an integrated system to curate ice and sediment cores. Under the umbrella of the national excellence equipment program CLIMCOR, we launched a reflexion about core curating and the management of associated fieldwork data. Our aim was then to conserve all data from fieldwork in an integrated cyber-environment which will evolve toward laboratory-acquired data storage in a near future. To do so, our demarche was conducted through an intimate relationship with field operators as well laboratory core curators in order to propose user-oriented solutions. The national core curating initiative proposes a single web portal in which all teams can store their fieldwork data. This portal is used as a national hub to attribute IGSNs. For legacy samples, this requires the establishment of a dedicated core list with associated metadata. However, for forthcoming core data, we developed a mobile application to capture technical and scientific data directly on the field. This application is linked with a unique coring-tools library and is adapted to most coring devices (gravity, drilling, percussion etc.) including multiple sections and holes coring operations. Those field data can be uploaded automatically to the national portal, but also referenced through international standards (IGSN and INSPIRE) and displayed in international portals (currently, NOAA’s IMLGS). In this paper, we present the architecture of the integrated system, future perspectives and the approach we adopted to reach our goals. We will also present our mobile application through didactic examples

The French initiative for scientific cores virtual curating : a user-orientedintegrated approach

PosterInternational audienceManaging scientific data is probably one the most challenging issue in modern science. The question is made evenmore sensitive with the need of preserving and managing high value fragile geological sam-ples: cores. Largeinternational scientific programs, such as IODP or ICDP are leading an intense effort to solve this problem andpropose detailed high standard work- and dataflows thorough core handling and curating. However most resultsderived from rather small-scale research programs in which data and sample management is generally managedonly locally – when it is . . .The national excellence equipment program (Equipex) CLIMCOR aims at developing French facilities for coringand drilling investigations. It concerns indiscriminately ice, marine and continental samples. As part of this initiative,we initiated a reflexion about core curating and associated coring-data management. The aim of the project isto conserve all metadata from fieldwork in an integrated cyber-environment which will evolve toward laboratoryacquireddata storage in a near future. In that aim, our demarche was conducted through an close relationship withfield operators as well laboratory core curators in order to propose user-oriented solutions.The national core curating initiative currently proposes a single web portal in which all scientifics teams can storetheir field data. For legacy samples, this will requires the establishment of a dedicated core lists with associatedmetadata. For forthcoming samples, we propose a mobile application, under Android environment to capture technicaland scientific metadata on the field. This application is linked with a unique coring tools library and is adaptedto most coring devices (gravity, drilling, percussion, etc...) including multiple sections and holes coring operations.Those field data can be uploaded automatically to the national portal, but also referenced through internationalstandards or persistent identifiers (IGSN, ORCID and INSPIRE) and displayed in international portals (currently,NOAA’s IMLGS).In this paper, we present the architecture of the integrated system, future perspectives and the approach we adoptedto reach our goals. We will also present in front of our poster, one of the three mobile applications, dedicated moreparticularly to the operations of continental drillings

The French initiative for scientific cores virtual curating : a user-orientedintegrated approach

PosterInternational audienceManaging scientific data is probably one the most challenging issue in modern science. The question is made evenmore sensitive with the need of preserving and managing high value fragile geological sam-ples: cores. Largeinternational scientific programs, such as IODP or ICDP are leading an intense effort to solve this problem andpropose detailed high standard work- and dataflows thorough core handling and curating. However most resultsderived from rather small-scale research programs in which data and sample management is generally managedonly locally – when it is . . .The national excellence equipment program (Equipex) CLIMCOR aims at developing French facilities for coringand drilling investigations. It concerns indiscriminately ice, marine and continental samples. As part of this initiative,we initiated a reflexion about core curating and associated coring-data management. The aim of the project isto conserve all metadata from fieldwork in an integrated cyber-environment which will evolve toward laboratoryacquireddata storage in a near future. In that aim, our demarche was conducted through an close relationship withfield operators as well laboratory core curators in order to propose user-oriented solutions.The national core curating initiative currently proposes a single web portal in which all scientifics teams can storetheir field data. For legacy samples, this will requires the establishment of a dedicated core lists with associatedmetadata. For forthcoming samples, we propose a mobile application, under Android environment to capture technicaland scientific metadata on the field. This application is linked with a unique coring tools library and is adaptedto most coring devices (gravity, drilling, percussion, etc...) including multiple sections and holes coring operations.Those field data can be uploaded automatically to the national portal, but also referenced through internationalstandards or persistent identifiers (IGSN, ORCID and INSPIRE) and displayed in international portals (currently,NOAA’s IMLGS).In this paper, we present the architecture of the integrated system, future perspectives and the approach we adoptedto reach our goals. We will also present in front of our poster, one of the three mobile applications, dedicated moreparticularly to the operations of continental drillings

The French initiative for scientific cores virtual curating : a user-oriented integrated approach

PosterInternational audienceManaging scientific data is a crucial issue for modern science. This concerns particularly the conservation of high value geological samples: cores. International scientific programs are leading an intense effort to solve this problem and propose detailed high standard work- and dataflows including core handling and curating. However, there is currently no consensual standard for sample and associated metadata management. The national excellence equipment program CLIMCOR aims at developing French facilities for scientific coring (ice, marine and continental). As part of it, we led a reflexion about cores and associated metada curating. Our aim is to conserve all metadata from fieldwork in an integrated cyber-environment which could evolve toward laboratory-acquired data storage. In that aim, our demarche was conducted through a close relationship with field operators and core curators, in order to propose user-oriented solutions.The national core curating initiative currently proposes a single web portal to store field data. For forthcoming samples, we propose a mobile application to capture technical and scientific metadata on the field or in cruise. This application is linked with a unique coring tools library and is adapted to most coring devices, including multiple sections and holes coring operations.Those field data can be uploaded automatically to the national portal, but also referenced through international standards or persistent identifiers (IGSN - SESAR, ORCID) and INSPIRE schema and displayed in international portals (currently, NOAA IMLGS).In this paper, we present the architecture of the integrated system, future perspectives and the approach we adopted to reach our goals.(1) http://climcor-equipex.dt.insu.cnrs.fr/?lang=e

Detection of live M. bovis BCG in tissues and IFN-γ responses in European badgers (Meles meles) vaccinated by oropharyngeal instillation or directly in the ileum

International audienceBackgroundOral vaccination with Mycobacterium bovis Bacille of Calmette and Guerin (BCG) has provided protection against M. bovis to badgers both experimentally and in the field. There is also evidence suggesting that the persistence of live BCG within the host is important for maintaining protection against TB. Here we investigated the capacity of badger inductive mucosal sites to absorb and maintain live BCG. The targeted mucosae were the oropharyngeal cavity (tonsils and sublingual area) and the small intestine (ileum).ResultsWe showed that significant quantities of live BCG persisted within badger in tissues of vaccinated badgers for at least 8 weeks following oral vaccination with only very mild pathological features and induced the circulation of IFNγ-producing mononuclear cells. The uptake of live BCG by tonsils and drainage to retro-pharyngeal lymph nodes was repeatable in the animal group vaccinated by oropharyngeal instillation whereas those vaccinated directly in the ileum displayed a lower frequency of BCG detection in the enteric wall or draining mesenteric lymph nodes. No faecal excretion of live BCG was observed, including when BCG was delivered directly in the ileum.ConclusionsThe apparent local loss of BCG viability suggests an unfavorable gastro-enteric environment for BCG in badgers, which should be taken in consideration when developing an oral vaccine for use in this species